The research of the CUCKOO Workgroup

1. Sequence-based prediction of post-translational modifications (PTMs).

Developing sequence-based predictors for various PTMs with a in-house developed algorithms.

(1) GPS: prediction of kinase-specific phosphorylation sites in GPS algorithm.

(2) PPSP: prediction of kinase-specific phosphorylation sites in Bayesian Decision Theory (BDT) algorithm.

(3) CSS-PALM: prediction of Palmitoylation sites.

(4) GPS-SUMO: prediction of sumoylation and sumo-binding sites.

(5) GPS-SNO: prediction of nitrosylation sites.

(6) GPS-YNO2: prediction of tyrosine nitration sites.

(7) GPS-CCD: prediction of calpain cleavage sites.

(8) GPS-Polo: prediction of PLK phosphorylation and phospho-binding sites.

(9) GPS-PUP: prediction of pupylation sites.

(10) GPS-ARM: prediction of APC/C recognization motifs.

(11) GPS-TSP: prediction of tyrosine sulfation sites.

(12) GPS-MBA: prediction of MHC-binding sites.

(13) GPS-MSP: prediction of methylated lysine and arginine sites.

2. Resource construction for PTMs.

Developing databases for various PTMs to host data resources of substrates, sites and enzymes.

(1) PLMD: Database of lysine modification sites.

(2) EKPD: Eukaryotic Kinase and Phosphatase Database.

(3) iUUCD: Ubiquitin and Ubiquitin-like Conjugation Database.

(4) MiCroKiTS: Database of proteins for Midbody, Centrosome, Kinetochore, Telomere and Spindle .

(5) pTestis: Database of phosphorylation sites in testis.

(6) CGDB: Database of phosphorylation sites in testis.

(7) WERAM: Eukaryotic writers, erasers and readers protein of histone acetylation and methylation system database.

(8) dbPPT: Database of phosphorylation sites in plants.

(9) dbPSP: Database of phosphorylation sites in prokaryotes.

(10) dbPAF: Database of phosphorylation sites in animals and fungi.

3. Network studies for PTMs.

Developing tools to (re)construct PTMs networks to dissect the cellular singalling.

(1) iGPS: GPS algorithm with the interaction filter, or in vivo GPS.

4. The relation between PTMs and genetic variations.

Analyzing the genetic variations which influence PTMs.

(1) PhosSNP: Phosphorylation-related SNP.